FALSE R version 4.0.2 (2020-06-22)
FALSE Platform: x86_64-apple-darwin17.0 (64-bit)
FALSE Running under: macOS Catalina 10.15.6
FALSE 
FALSE Matrix products: default
FALSE BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.0.dylib
FALSE LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
FALSE 
FALSE locale:
FALSE [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
FALSE 
FALSE attached base packages:
FALSE [1] stats     graphics  grDevices utils     datasets  methods   base     
FALSE 
FALSE other attached packages:
FALSE  [1] cbmbtools_0.0.0.9034 vegan_2.5-6          lattice_0.20-41     
FALSE  [4] permute_0.9-5        ggpubr_0.4.0         RColorBrewer_1.1-2  
FALSE  [7] knitr_1.29           scales_1.1.1         tidyselect_1.1.0    
FALSE [10] forcats_0.5.0        stringr_1.4.0        dplyr_1.0.1         
FALSE [13] purrr_0.3.4          readr_1.3.1          tidyr_1.1.1         
FALSE [16] tibble_3.0.3         ggplot2_3.3.2        tidyverse_1.3.0     
FALSE 
FALSE loaded via a namespace (and not attached):
FALSE  [1] httr_1.4.2        jsonlite_1.7.0    splines_4.0.2     carData_3.0-4    
FALSE  [5] modelr_0.1.8      assertthat_0.2.1  blob_1.2.1        cellranger_1.1.0 
FALSE  [9] yaml_2.2.1        pillar_1.4.6      backports_1.1.8   glue_1.4.1       
FALSE [13] digest_0.6.25     ggsignif_0.6.0    rvest_0.3.6       colorspace_1.4-1 
FALSE [17] htmltools_0.5.0   Matrix_1.2-18     pkgconfig_2.0.3   broom_0.7.0      
FALSE [21] haven_2.3.1       openxlsx_4.1.5    rio_0.5.16        mgcv_1.8-31      
FALSE [25] generics_0.0.2    car_3.0-9         ellipsis_0.3.1    withr_2.2.0      
FALSE [29] cli_2.0.2         magrittr_1.5      crayon_1.3.4      readxl_1.3.1     
FALSE [33] evaluate_0.14     fs_1.5.0          fansi_0.4.1       nlme_3.1-148     
FALSE [37] MASS_7.3-51.6     rstatix_0.6.0     xml2_1.3.2        foreign_0.8-80   
FALSE [41] tools_4.0.2       data.table_1.13.0 hms_0.5.3         lifecycle_0.2.0  
FALSE [45] munsell_0.5.0     reprex_0.3.0      cluster_2.1.0     zip_2.0.4        
FALSE [49] compiler_4.0.2    rlang_0.4.7       grid_4.0.2        rstudioapi_0.11  
FALSE [53] rmarkdown_2.3     codetools_0.2-16  gtable_0.3.0      abind_1.4-5      
FALSE [57] DBI_1.1.0         curl_4.3          R6_2.4.1          lubridate_1.7.9  
FALSE [61] stringi_1.4.6     parallel_4.0.2    Rcpp_1.0.5        vctrs_0.3.2      
FALSE [65] dbplyr_1.4.4      xfun_0.16

FALSE 
FALSE   Kruskal-Wallis rank sum test
FALSE 
FALSE data:  Gene_16S_copies_per_mL by Sample_Type
FALSE Kruskal-Wallis chi-squared = 29.276, df = 6, p-value = 5.394e-05
FALSE 
FALSE 
FALSE   Pairwise comparisons using Wilcoxon rank sum exact test 
FALSE 
FALSE data:  ddpcr$Gene_16S_copies_per_mL and ddpcr$Sample_Type 
FALSE 
FALSE               NTC     Iso_Ctrl PBS     Syringe_Rinse Homog_Ctrl BAL    
FALSE Iso_Ctrl      0.64000 -        -       -             -          -      
FALSE PBS           0.58947 0.40000  -       -             -          -      
FALSE Syringe_Rinse 0.42353 0.03333  0.40000 -             -          -      
FALSE Homog_Ctrl    0.58947 0.16667  0.42353 0.40000       -          -      
FALSE BAL           0.22238 0.00839  0.31818 0.27082       0.90909    -      
FALSE Lung          0.00839 0.00262  0.07955 0.00839       0.07955    0.00023
FALSE 
FALSE P value adjustment method: BH

Quality Checks

III. Confirmation of Sufficient Reads

3.1 MiSeq Reads by Sample Type

## 3.2 OTU Counts by Sample Type

IV. Principal Component Analysis

FALSE 
FALSE Call:
FALSE adonis(formula = adonis.hel.df.wbn ~ otu.df.lungsamp.sampctrls$RA_Groups,      permutations = 10000, method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                                     Df SumsOfSqs MeanSqs F.Model      R2
FALSE otu.df.lungsamp.sampctrls$RA_Groups  2    3.8879 1.94394  2.3806 0.16554
FALSE Residuals                           24   19.5980 0.81658         0.83446
FALSE Total                               26   23.4859                 1.00000
FALSE                                        Pr(>F)    
FALSE otu.df.lungsamp.sampctrls$RA_Groups 9.999e-05 ***
FALSE Residuals                                        
FALSE Total                                            
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
FALSE 
FALSE Call:
FALSE adonis(formula = adonis.hel.bl ~ adonis.otudf.bl$Sample_Type,      permutations = 10000, method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                             Df SumsOfSqs MeanSqs F.Model      R2    Pr(>F)    
FALSE adonis.otudf.bl$Sample_Type  1    2.4484  2.4484  3.1334 0.15563 9.999e-05 ***
FALSE Residuals                   17   13.2838  0.7814         0.84437              
FALSE Total                       18   15.7323                 1.00000              
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
FALSE 
FALSE Call:
FALSE adonis(formula = adonis.hel.wn ~ adonis.otudf.wn$RA_Groups, permutations = 10000,      method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
FALSE adonis.otudf.wn$RA_Groups  1    2.4698 2.46976  3.3064 0.18061  2e-04 ***
FALSE Residuals                 15   11.2046 0.74697         0.81939           
FALSE Total                     16   13.6744                 1.00000           
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
FALSE 
FALSE Call:
FALSE adonis(formula = adonis.hel.bn ~ adonis.otudf.bn$Organ, permutations = 10000,      method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                       Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
FALSE adonis.otudf.bn$Organ  1    0.9148 0.91483 0.99522 0.05856 0.4649
FALSE Residuals             16   14.7076 0.91922         0.94144       
FALSE Total                 17   15.6224                 1.00000

FALSE 
FALSE Call:
FALSE adonis(formula = otu.good.lungsamp.isoctrls_hel ~ otu.df.lungsamp.isoctrls$Sample_Type,      permutations = 10000, method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                                      Df SumsOfSqs MeanSqs F.Model     R2
FALSE otu.df.lungsamp.isoctrls$Sample_Type  3    5.0693  1.6898  2.0376 0.1846
FALSE Residuals                            27   22.3910  0.8293         0.8154
FALSE Total                                30   27.4603                 1.0000
FALSE                                         Pr(>F)    
FALSE otu.df.lungsamp.isoctrls$Sample_Type 9.999e-05 ***
FALSE Residuals                                         
FALSE Total                                             
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
FALSE 
FALSE Call:
FALSE adonis(formula = adonis.hel.il ~ adonis.otudf.il$RA_Groups, permutations = 10000,      method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                           Df SumsOfSqs MeanSqs F.Model      R2    Pr(>F)    
FALSE adonis.otudf.il$RA_Groups  1    2.6804 2.68040  3.4196 0.15253 9.999e-05 ***
FALSE Residuals                 19   14.8927 0.78383         0.84747              
FALSE Total                     20   17.5731                 1.00000              
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
FALSE 
FALSE Call:
FALSE adonis(formula = adonis.hel.ib ~ adonis.otudf.ib$RA_Groups, permutations = 10000,      method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                           Df SumsOfSqs MeanSqs F.Model      R2  Pr(>F)  
FALSE adonis.otudf.ib$RA_Groups  1    1.2087 1.20866  1.3141 0.06165 0.06999 .
FALSE Residuals                 20   18.3957 0.91978         0.93835          
FALSE Total                     21   19.6044                 1.00000          
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

FALSE 
FALSE Call:
FALSE adonis(formula = otu.good.lungsamp.seqctrls_hel ~ otu.df.lungsamp.seqctrls$Sample_Type,      permutations = 10000, method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                                      Df SumsOfSqs MeanSqs F.Model      R2
FALSE otu.df.lungsamp.seqctrls$Sample_Type  3     7.919 2.63959  3.2847 0.16193
FALSE Residuals                            51    40.984 0.80361         0.83807
FALSE Total                                54    48.903                 1.00000
FALSE                                         Pr(>F)    
FALSE otu.df.lungsamp.seqctrls$Sample_Type 9.999e-05 ***
FALSE Residuals                                         
FALSE Total                                             
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
FALSE 
FALSE Call:
FALSE adonis(formula = adonis.hel.sl ~ adonis.otudf.sl$RA_Groups, permutations = 10000,      method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                           Df SumsOfSqs MeanSqs F.Model      R2    Pr(>F)    
FALSE adonis.otudf.sl$RA_Groups  1     4.146  4.1459  5.1613 0.10717 9.999e-05 ***
FALSE Residuals                 43    34.541  0.8033         0.89283              
FALSE Total                     44    38.687                 1.00000              
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
FALSE 
FALSE Call:
FALSE adonis(formula = adonis.hel.sb ~ adonis.otudf.sb$RA_Groups, permutations = 10000,      method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                           Df SumsOfSqs MeanSqs F.Model      R2    Pr(>F)    
FALSE adonis.otudf.sb$RA_Groups  1     2.069 2.06931  2.3933 0.05159 0.0006999 ***
FALSE Residuals                 44    38.044 0.86463         0.94841              
FALSE Total                     45    40.113                 1.00000              
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

FALSE 
FALSE Call:
FALSE adonis(formula = otu.good.tong.lungsamp_hel ~ otu.df.tong.lungsamp$Sample_Type,      permutations = 10000, method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                                  Df SumsOfSqs MeanSqs F.Model      R2    Pr(>F)
FALSE otu.df.tong.lungsamp$Sample_Type  2    3.9663 1.98317  2.6355 0.12772 9.999e-05
FALSE Residuals                        36   27.0894 0.75248         0.87228          
FALSE Total                            38   31.0557                 1.00000          
FALSE                                     
FALSE otu.df.tong.lungsamp$Sample_Type ***
FALSE Residuals                           
FALSE Total                               
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
FALSE 
FALSE Call:
FALSE adonis(formula = adonis.hel.tl ~ adonis.otudf.tl$Sample_Type,      permutations = 10000, method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                             Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)  
FALSE adonis.otudf.tl$Sample_Type  1     1.039 1.03903  1.5005 0.05265 0.0133 *
FALSE Residuals                   27    18.696 0.69244         0.94735         
FALSE Total                       28    19.735                 1.00000         
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
FALSE 
FALSE Call:
FALSE adonis(formula = adonis.hel.tb ~ adonis.otudf.tb$Sample_Type,      permutations = 10000, method = "euclidean") 
FALSE 
FALSE Permutation: free
FALSE Number of permutations: 10000
FALSE 
FALSE Terms added sequentially (first to last)
FALSE 
FALSE                             Df SumsOfSqs MeanSqs F.Model      R2    Pr(>F)    
FALSE adonis.otudf.tb$Sample_Type  1    2.6012 2.60116  3.2809 0.10489 9.999e-05 ***
FALSE Residuals                   28   22.1989 0.79282         0.89511              
FALSE Total                       29   24.8001                 1.00000              
FALSE ---
FALSE Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

V. Diversity Indices

5.1 Alpha Diversity

FALSE   Tukey multiple comparisons of means
FALSE     95% family-wise confidence level
FALSE 
FALSE Fit: aov(formula = tukey_otu_df[, "Unique_Otus_per_1k_reads"] ~ tukey_otu_df[, "Alpha_Div_Groups"])
FALSE 
FALSE $`tukey_otu_df[, "Alpha_Div_Groups"]`
FALSE                                            diff        lwr         upr
FALSE Isolation Control-BAL                -10.612291 -27.006526   5.7819429
FALSE Lung-BAL                              25.049970   7.457534  42.6424053
FALSE Sampling Control-BAL                  -2.528455 -20.690372  15.6334619
FALSE Sequencing Control-BAL               -13.515401 -27.202081   0.1712778
FALSE Lung-Isolation Control                35.662261  18.778539  52.5459833
FALSE Sampling Control-Isolation Control     8.083837  -9.392476  25.5601491
FALSE Sequencing Control-Isolation Control  -2.903110 -15.666004   9.8597843
FALSE Sampling Control-Lung                -27.578425 -46.183380  -8.9734692
FALSE Sequencing Control-Lung              -38.565371 -52.834721 -24.2960216
FALSE Sequencing Control-Sampling Control  -10.986946 -25.952766   3.9788736
FALSE                                          p adj
FALSE Isolation Control-BAL                0.3746804
FALSE Lung-BAL                             0.0014826
FALSE Sampling Control-BAL                 0.9950044
FALSE Sequencing Control-BAL               0.0545862
FALSE Lung-Isolation Control               0.0000011
FALSE Sampling Control-Isolation Control   0.6949822
FALSE Sequencing Control-Isolation Control 0.9684857
FALSE Sampling Control-Lung                0.0008519
FALSE Sequencing Control-Lung              0.0000000
FALSE Sequencing Control-Sampling Control  0.2510366

FALSE   Tukey multiple comparisons of means
FALSE     95% family-wise confidence level
FALSE 
FALSE Fit: aov(formula = tukey_otu_df[, "Shannon"] ~ tukey_otu_df[, "Alpha_Div_Groups"])
FALSE 
FALSE $`tukey_otu_df[, "Alpha_Div_Groups"]`
FALSE                                            diff        lwr        upr     p adj
FALSE Isolation Control-BAL                -0.9947478 -1.8514868 -0.1380087 0.0147639
FALSE Lung-BAL                              0.6346623 -0.2846930  1.5540176 0.3098538
FALSE Sampling Control-BAL                 -0.5859416 -1.5350572  0.3631740 0.4234102
FALSE Sequencing Control-BAL               -1.2226705 -1.9379166 -0.5074244 0.0000876
FALSE Lung-Isolation Control                1.6294101  0.7470911  2.5117290 0.0000205
FALSE Sampling Control-Isolation Control    0.4088062 -0.5044807  1.3220931 0.7201786
FALSE Sequencing Control-Isolation Control -0.2279227 -0.8948932  0.4390477 0.8732743
FALSE Sampling Control-Lung                -1.2206039 -2.1928720 -0.2483357 0.0067338
FALSE Sequencing Control-Lung              -1.8573328 -2.6030284 -1.1116372 0.0000000
FALSE Sequencing Control-Sampling Control  -0.6367289 -1.4188211  0.1453633 0.1637833

5.2 Beta Diversity

FALSE 
FALSE   Pairwise comparisons using Wilcoxon rank sum test with continuity correction 
FALSE 
FALSE data:  bray_dist_lbtce_long_mut_filt$BC_Index and bray_dist_lbtce_long_mut_filt$Sample_Type 
FALSE 
FALSE        BAL     Blank   Cecum   Lung  
FALSE Blank  0.0074  -       -       -     
FALSE Cecum  < 2e-16 < 2e-16 -       -     
FALSE Lung   < 2e-16 3.7e-11 < 2e-16 -     
FALSE Tongue < 2e-16 < 2e-16 < 2e-16 0.0001
FALSE 
FALSE P value adjustment method: BH

FALSE 
FALSE   Wilcoxon rank sum exact test
FALSE 
FALSE data:  BC_Index by Comparison_Type
FALSE W = 85, p-value = 0.0004114
FALSE alternative hypothesis: true location shift is not equal to 0

VI. Relative Abundance